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From: Jag Silwal <jagsilwal.gmail.com>

Date: Fri, 19 Jan 2018 16:17:03 -0500

Dan,

Thanks for your email. I will give it a try. I will also try in another

protein to verify this.

But am I using the mask correctly here? Basically, I am trying to

calculate the angle between two helices by choosing a common atom (2316)

from the loop region that connects two helices. Is this how its commonly

done? I just wanted to make sure I am correct on this one before I do other

calculations.

Thank you again!!

Sincerely,

Jag

On Fri, Jan 19, 2018 at 3:24 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:

*> Tough to really say what might be going on here without seeing the
*

*> system. One thing I like to do in these situations is actually
*

*> visualize the vectors themselves. You can do this by writing the
*

*> vector data out in 'vectraj' (vector pseudo-trajectory) format, like
*

*> so:
*

*>
*

*> vector Helix1 .2018 @2316
*

*> vector Helix2 .2316 @22841
*

*> run
*

*> writedata vectors.nc vectraj Helix1 Helix2 trajfmt netcdf parmout
*

*> vectors.parm7
*

*>
*

*> Then you can visualize what the 'vector' commands are actually
*

*> calculating and see if those are good representations of your helices.
*

*>
*

*> Hope this helps,
*

*>
*

*> -Dan
*

*>
*

*> On Fri, Jan 19, 2018 at 1:23 PM, Jag Silwal <jagsilwal.gmail.com> wrote:
*

*> > Dear all,
*

*> > I want to measure the angle between two helices in a protein for the
*

*> > entire simulation (angle Vs time). I found the following guide from Dan
*

*> and
*

*> > I followed it and ran a sample run for one of the helices. I got the
*

*> > results and everything but the angle is almost double what I was
*

*> expecting
*

*> > for the entire run.
*

*> > So, I think I mightn't be using 'atom mask' properly here. So the two
*

*> > helices are connected by a small loop with the turn of about 50 degrees.
*

*> If
*

*> > the starting of one helix is residue 'A' then turns at residue 'B' and
*

*> > continues as another helix which ends at residue 'C', can I use the mask
*

*> as
*

*> > follows:
*

*> > vector Helix1 .2018 @2316
*

*> > vector Helix2 .2316 @22841
*

*> > Where, *the numbers are the C-alpha atom number for residues A, B and C.*
*

*> >
*

*> > Did I do this right?
*

*> >
*

*> > Any insight would be helpful.
*

*> >
*

*> > Sincerely,
*

*> > Jag
*

*> > ............................................................
*

*> ............................................................
*

*> ...............
*

*> > One thing you can try is calculating the angle between the vectors that
*

*> run
*

*> > along the helices; this can be done with cpptraj. First, read in your
*

*> > topology and trajectory:
*

*> > parm MyParm.parm7
*

*> > trajin MyTraj.nc <https://www.researchgate.net/
*

*> deref/http%3A%2F%2FMyTraj.nc>
*

*> > Then you would create the vectors:
*

*> > vector Helix1 <mask1> <mask2>
*

*> > vector Helix2 <mask3> <mask4>
*

*> > Here, mask1 and mask2 are atom masks defining each end of the first helix
*

*> > and mask3 and mask4 are atom masks defining each end of the second helix.
*

*> > Then you can use the 'vectormath' analysis command to calculate the angle
*

*> > between the vectors:
*

*> > vectormath vec1 Helix1 vec2 Helix2 dotangle out H1-H2-angle.dat
*

*> > Hope this helps,
*

*> > -Dan
*

*> > _______________________________________________
*

*> > AMBER mailing list
*

*> > AMBER.ambermd.org
*

*> > http://lists.ambermd.org/mailman/listinfo/amber
*

*>
*

*>
*

*>
*

*> --
*

*> -------------------------
*

*> Daniel R. Roe
*

*> Laboratory of Computational Biology
*

*> National Institutes of Health, NHLBI
*

*> 5635 Fishers Ln, Rm T900
*

*> Rockville MD, 20852
*

*> https://www.lobos.nih.gov/lcb
*

*>
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

*> http://lists.ambermd.org/mailman/listinfo/amber
*

*>
*

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Received on Fri Jan 19 2018 - 13:30:04 PST

Date: Fri, 19 Jan 2018 16:17:03 -0500

Dan,

Thanks for your email. I will give it a try. I will also try in another

protein to verify this.

But am I using the mask correctly here? Basically, I am trying to

calculate the angle between two helices by choosing a common atom (2316)

from the loop region that connects two helices. Is this how its commonly

done? I just wanted to make sure I am correct on this one before I do other

calculations.

Thank you again!!

Sincerely,

Jag

On Fri, Jan 19, 2018 at 3:24 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:

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Received on Fri Jan 19 2018 - 13:30:04 PST

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